Evidence would show Blowers breached police drug storage protocols in the days before by moving the methamphetamine to a different storage area to which he had access, Hamlin said.
Prior to that raid police had already undertaken an employment investigation into failures by Blowers to account for drugs he was in charge of. But it wasn't suspected that he was stealing at that time, Mr Hamlin said.
Blowers is accused of using his position as head of the organised crime unit to steal drugs from the police drug storage lock up.
Blowers' defence counsel, Arthur Fairley, told the court his client strongly denied the accusations but would admit he made a lapse in judgment trusting the person named as his associate.
"Protocols are one thing but what happens in practice is another," Mr Fairley said.
The trial is set for two weeks and is expected to hear from 40 witnesses, mostly police.